☰ Navigation Tabs
Crystal structure of Na+ bound Peptidyl-tRNA Hydrolase from Acinetobacter baumannii at 2.19 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JY7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 100 mM NaHEPES pH 7.5
25% PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.62 53.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.29 α = 90 b = 58.75 β = 90 c = 109.21 γ = 90
Symmetry Space Group P 21 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 300 PIXEL DECTRIS PILATUS3 6M 2018-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9537 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.19 54.6 98.7 0.165 0.176 0.058 8.7 9.1 11810 37.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.19 2.23 97 0.8 0.935 0.301 2.2 9.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4JY7 2.19 54.6 11810 567 98.7 0.17708 0.17408 0.184 0.23406 0.2395 RANDOM 37.5
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.12 0.03 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.64 r_dihedral_angle_3_deg 14.513 r_dihedral_angle_4_deg 11.508 r_long_range_B_refined 9.266 r_long_range_B_other 8.872 r_dihedral_angle_1_deg 6.564 r_scangle_other 5.902 r_mcangle_other 4.295 r_mcangle_it 4.292 r_scbond_it 3.831
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.64 r_dihedral_angle_3_deg 14.513 r_dihedral_angle_4_deg 11.508 r_long_range_B_refined 9.266 r_long_range_B_other 8.872 r_dihedral_angle_1_deg 6.564 r_scangle_other 5.902 r_mcangle_other 4.295 r_mcangle_it 4.292 r_scbond_it 3.831 r_scbond_other 3.831 r_mcbond_it 2.959 r_mcbond_other 2.948 r_angle_refined_deg 1.732 r_angle_other_deg 1.056 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1476 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing